Torchwood Classified Files
by Sandylee007
Summary: SCENES MISSING FROM THE SERIES. There was a lot of the story of Jack Harkness and Ianto Jones that we didn't get to see. Moments of horrible heartbreak, sweet love and bitter arguments. These oneshots unfold the classified parts of their lovestory. SLASH JANTO ALL GENRES INCLUDED, REQUESTS VERY MUCH ACCEPTED!
1. S1, E4: Souls Left Behind

A/N: Sooooooo… Amongst the furious process of sorting out another project this idea began to cook up in my head. There are several 'missing scenes' in my head, majorily Ianto and Jack centric, and I've just gotta let some of them out.

GENRES: ANYTHING AND EVERYTHING! From angst to fluff. REQUESTS VERY, VERY WELCOMED!

DISCLAIMER: Oh, please…! If I DID own something, Ianto, Owen and Tosh would've NEVER died. (growls, then clears throat) Er… Sorry 'bout that.

WARNINGS: SLASH, gore, adult themes, violence, some heartbreaking bits ahoy as well as a fluff that'll make your teeth ache… (glances around) WOAH! You sure can run fast…!

Awkay… It's go time, ain't it? I REALLY hope that you'll enjoy the ride.

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><p>SERIES 1, EPISODE 4 – Souls Lef Behind<p>

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><p>It was a horrible day. True, it could've ended even worse. Hell a lot worse. But as Jack Harkness finished the process of having Ianto Jones officially suspended and downed an unhealthily sharp drink he couldn't find a shred of gratitude. The drink didn't manage to wash away the bitter taste sitting stubbornly in his mouth.<p>

Ianto, the harmless invisible man who looked good in a suit and cleaned up their shit, had fooled them all. Fooled _him_. The coffee boy managed to hide something that should've belonged to nightmares into the hub, into Jack's only home. And Jack, who was supposed to be the leader of the team, didn't have a clue.

It was a blink of an eye from Suzie Costello and he hadn't learned a thing.

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><p> _"__When did you last ask me anything about my life?"_ /

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><p>Jack didn't have a clue that something so dangerous was happening. That Ianto was so in love that he was fighting a desperate war to keep her alive. So in love that the both of them suffering was better than losing her. How was Jack supposed to have seen any of that when he couldn't even remember the previous time he looked at Ianto properly?<p>

If Jack was fully honest with himself he wasn't entirely sure if whe was more furious with Ianto or himself.

Jack sighed, feeling utterly drained all of a sudden. Around then he became acutely aware of the fact that it'd been nine hours from when the Cyberwoman went down.

Tosh had been the first to leave, unable to watch Ianto's agony. Gwen followed quickly, guilt shining loud and clear in her anguished, teary eyes. Somehow her remorse only succeeded in adding fuel to Jack's fury. Owen stood there for quite a while, never once looking away from the Welshman. A couple of times the Londoner's lips parted but in the end the doctor walked away without a word. Jack could've sworn that Owen's shoulders were just a little bit slumped as he went.

Jack himself refused to feel guilt. Whoever the woman Ianto fell in love with was died the second her transformation began. This was a massive mess that needed to be taken care of, by any means necessary. Instead of addressing the grieving archivist he took the other's gun from the floor, then turned and left as well, not looking over his shoulder. He stormed into his office.

That was where Jack remained. Seething, trying to understand, so angry and betrayed that it quite nearly took his breath away. Desperately trying to decide what the hell it was that he was supposed to do.

After nine hours of replaying every single moment he'd shared with Ianto Jack finally had the answer.

He ordered the rest of the team to go home. They protested at first, reasoning that there was a load of sorting out to do in far more ways than one, but had no other choice but to relent. Jack himself headed towards where he last saw Ianto. What he found certainly wasn't what he'd expected.

The place that hours ago was bathing in blood had been cleaned up meticulously. Jack couldn't spot even a single stray drop. Three bodies lay on the floor, each of them in a entirely too familiar black bag. In the middle of it all stood Ianto. No longer crying or screaming, instead staring at the bags with eyes that chilled Jack. They were as dead as those hidden by plastic. The archivist, who still wore blood soaked clothes and hadn't washed his hands, was unhealthily pale. The young man's whole body was shaking under a thunderstorm of shock but he refused to sit down. And that was when Jack noticed the fourth, still empty body bag. It made him want to vomit.

Ianto's changed breathing pattern gave away that he'd noticed Jack's entrance. The captain waited for a few moments until he came to the conclusion that he'd have to make the first move. "You cleaned up", he observed in a cool, emotionally detached voice.

"Yes." Ianto's tone was frosty, professional. Those lifeless eyes didn't turn towards him. "I clean up my own shit." The Welshman then took a deep breath, straightening his posture. "Why don't we just skip this chit-chat and get it over with? We both know what you came here for."

Another violent assault of nausea went through Jack. Get it over with? He didn't let the discomfort show, though. Instead he took his gun and pointed it yet again.

He'd been doing far too much of that today.

Ianto's gaze didn't sway from the bodies. Yet as soon as Jack made his move the man seemed to relax, just a little bit. "I knew from the start that I wouldn't make it out alive if I'd get caught. I accepted it. Lisa… She was all that mattered and now…" The younger man's voice broke and he cleared his throat, blinking quickly. "According to the protocol you had two options in your hands. I knew which one you picked when I heard the others leaving."

Jack's jaw tightened. He'd expected fury, more shouting. He hadn't anticipated this resigned, eerie calm. This lack of fight. "Do you imagine that I'm enjoying this?" he snarled, sounding far more bitter than he'd intended.

Ianto shrugged. "You've already held a gun to my head twice today. You didn't seem very reluctant, then." Finally, finally those blue eyes met his. All of a sudden they were full of plea. "Remember what you said about threats? Just finish it."

Jack's heart was hammering while he stared at Ianto, the gun still held high against the Welshman. He'd taken a lot of lives over the course of his seemingly endless life. But this… This was different. Far more horrible. And there, looking into those hollow blue twin pools, Jack made what might just be his cruelest decision of the day. He lowered his gun and holstered it, unused.

It took a few moments before Ianto seemed to comprehend what his boss did. The man was so exhausted that the betrayal and rage that appeared were nothing but ghosts. "So that's it? You'll make me live?"

Jack nodded, his face somehow remaining a mask of steel despite that emotions raging inside. "Yeah. I'll make you live." He nearly let it slip that he'd already pulled Ianto back to life once just hours ago, kicking and screaming. He wasn't going to just…

Ianto swallowed loudly. It was impossible to read those eyes because there was nothing in them. "I… I fought so long and hard, trying to save her. And now… Because of my decision two people are dead. Your entire team could've died. All for nothing. Lisa… Lisa's gone. I'll… I'll have to live with that for the rest of my life." There was a brief, agonized pause. "Why won't you just let me go?"

Jack lifted his chin. His heart was thundering so hard that it was aching. The stench of blood, death and tears in the room was sickening. "One day… You'll understand."

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><p>Jack summoned Owen to drive Ianto home a couple of hours later and ordered the doctor to stay with the shattered man until it'd be safe to leave him alone. Owen expressed loud displeasure over the assignment but eventually succumbed to his fate. None of the three would look at each other while the two took their silent leave and Jack returned to complete a monster of paperwork. Somehow, impossibly, feeling old and weary beyond his years<p>

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><p>Three days passed by before Owen marched into Jack's office without bothering to knock. The doctor's pale, distraught face was a picture of fury. "The next fucking time you make me keep a suicide watch… I'll quit and take enough Retcon to send me back to puberty", the Londoner snarled. Then left, slamming the door.<p>

Jack was still too consumed by his own, raw anger to understand why he wanted to cry.

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><p>Eventually, the suspension over and with nowhere else to go, Ianto returned. On that day his gaze met Jack's, locked and held. They exchanged grim nods, a signal that yes, Ianto understood, now.<p>

Sometimes letting a person survive being left behind is the most bitter punishment of all.

It was much too soon, for both of them, to see it as a second chance.

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><p>End of scene.<p>

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><p>AN: Well… (takes a deep breath) THAT was dark. GOSH, that episode…! If we wouldn't already know what's up ahead…

Sooooooo… Thoughts? Comments? Requests? PLEASE, do let me know! I'm more than eager to hear.

In any case, thank you so much for the reading! And who knows. Perhaps we'll cross paths again?

Take care!


	2. S1, E6: And I saw you for the first time

A/N: I'm baack! And with a new deleted scene, no less. Yosh?

THANK YOU, so much, for all your reviews and listings! It makes me insanely happy this story's already gained friends. (HUGS)

Awkay, because I reeeeeeeeally should be hurrying elsewhere already… Let's go! I really hope that you'll enjoy the ride.

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><p>SERIES 1, EPISODE 6 – 'And I saw you for the first time'<p>

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><p>Well, the team's bonding experience certainly didn't go swimmingly. One got shot. Two more were captured by cannibals. It came very, very close that lives weren't lost.<p>

But, Jack mused with a macabre little hint of bitter amusement, it seemed to have worked on some level, just a little bit.

Gwen, who'd been checked over and announced to have been properly patched up by Owen, stood nearby Tosh and Ianto with a worried look on her face. Owen also lingered nearby, his arms folded and appearing so throughoutly fed up that it might've been amusing under different circumstances. Tosh, who seemed pale and shaken as she stood there trembling slightly, hadn't let go of Ianto's hand since the Welshman had been unleashed from the clutches of the paramedics. Ianto himself seemed barely able to stand. The hazy look in his eyes suggested that he was somewhere very far away.

Jack's mind was entirely too eager to repeat the list of injuries he'd received from the paramedics. A concussion. Several damaged, at least cracked ribs that they would've wanted to check over properly but the stubborn young man adamantly refused to go to a hospital. Countless of horrible bruises.

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><p> _"They… They said that they'd tenderise the meat", Tosh told him while Ianto was still under inspection. She gulped loudly, wrapping her arms tightly around herself, and refused to look at him. "He… He told me to run. __So… __I did." She wiped at her eyes harshly, obviously barely able to hold back a sob. She looked away even more pointedly. __"I… __I just left him there. All alone. He tried to save me and I left him there to be tenderised!" _/

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><p><em>So did I<em>, Jack mused, unable to erase the awful taste sitting in his mouth.

But now wasn't the time to worry about that. He had a exhausted, traumatized team to get away from the set of a horror movie. He made his way to them with his usual aura of leadership. He didn't even try to smile. "So… Home?"

They all nodded eagerly.

"Oh yeah, and team?" He glanced over his shoulder as the rest of them clambered to the vehicle. "Consider the next three days off unless it's the end of the world."

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><p>Jack dropped the rest of the team to the hub. Ianto, who'd been fighting against the intense urge to fall asleep throughout the ride, barely noticed this. They said their byes without exchanging much of a word, all of them too tired to talk.<p>

Ianto was about to take his own leave, blatantly ignoring the fact that he could barely move enough to get out of the car. Jack's voice stopped him. "Where do you think you're going?"

Ianto froze. He kept his eyes fixed on his hand, which had already been placed to the door handle. "Home, sir." Was that his voice?

All he wanted was to crawl into his own bed, even if he wouldn't dare to sleep. To just lay down in the comfort of his own home. Maybe it'd be enough to convince him that the cannibals weren't going to lay their hands or teeth on him.

"You have a nasty concussion, Ianto", Jack pointed out. "The waking up every couple of hours and all that, remember? So… Either it's spending the night in my company or in a hospital. Which one do you choose?"

Ianto stiffened completely, even if the agony it caused made him want to scream. He gritted his teeth, feeling trapped. He didn't want Jack to his home, to his own personal territory. He didn't want to spend that much time alone with Jack, for far more reasons than his head was able to process at the moment. But… He also didn't want to go to a hospital, to be urder the mercy of some more total strangers.

In the end he inhaled a sharp breath that hurt hellishly. "Home", he murmured. Hoping that the words didn't sound as venomous as he felt.

He could've sworn that he felt eyes on him, for just a moment, but didn't look to make sure. "Home it is, then." With that Jack started the car.

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><p>The first descriptive word that came to Jack's mind as he looked at Ianto's small apartment was 'clean'. He wasn't exactly surprised. There was fairly little furniture and even less ornaments. There wasn't much but what little remained had been chosen with an excellent taste. The empty spots here and there spoke of items that'd been cast aside. He felt a sharp twinge inside at an empty spot that clearly used to be a framed photograph. He didn't have to wonder long to figure out who'd been in the picture.<p>

If Jack had been forced to make a psychological profile on the person who lived there he wouldn't have been able to. Ianto Jones, the invisible man. Even in his own home.

Jack was pulled out of his thoughts when he felt Ianto's trembling intensify. Even with leaning heavily against him the archivist had been barely able to walk long enough to get here. It was only a matter of time before the younger man's knees would buckle.

"Right." Jack took a deep breath, then focused on his patient and wondered how the hell they ended up into this situation. "Which one first? Something to eat, a bath or bed?"

For a moment something between horror and nausea flashed in Ianto's eyes. "Bed", the young man announced. The voice hinted that both of the other options were unacceptable at the moment.

Jack nodded. "Let's get moving, then." He fought the urge to wince when he could just tell how much ache each motion pushed through Ianto. He wasn't able to smother the onslaught of guilt that rushed over him.

Today wasn't his best day as a teamleader, was it?

It was a slow, incredibly painful and in far more ways than one uncomfortable process. But eventually Ianto lay in bed, a sheen of cold sweat on his forehead, trembling to the core of his being and visibly fighting hard not to gasp or throw up. On the brink of passing out, no doubt.

Now Jack did wince. "I should've taken you to a hospital", he growled. Unsure which one of them he was more frustrated at.

"NO!" Ianto snarled back with as much volume as he could still muster. The man shook his head, then winced. "Don't you dare…!"

Jack spread his hands as a sign of surrender. "I won't, I won't." _Yet, at least._ He stood beside the bed, not quite sure what he was supposed to do. Somehow crawling on it, with Ianto so vulnerable and showing clear 'keep out' signals, would've felt like a violation. He also couldn't quite bring himself to leave the room just yet.

"What you did today, for Tosh…" Jack paused for a second. "It was very brave."

"No, it wasn't." There was a hint of moisture in Ianto's eyes but no tears spilled. "I… Before she woke up… I waited for you. I thought to myself that at any moment you'd come for her. Eventually I realized that you wouldn't. So… I had to try something myself." The archivist, who'd just been to his first field mission, shrugged although it had to hurt. "I had to give it a shot."

Jack stood perfectly still, trying to overcome the feel that he'd just been stabbed. Never a pleasant experience. Then, with gentleness he hadn't expected, he outstretched a hand and caressed Ianto's hair, carefully avoiding the bruises and bumps. A hint of warmth swell inside when the younger man didn't pull away. "I always come for you. Always. I'm just… I'm so sorry that it took so long today." With that, feeling that he'd said everything that could possibly make any difference, he turned and began to head towards the living room. Until he paused by the doorway. "And Ianto? I am sorry about Lisa." With that he left the room, feeling a pair of eyes watching him.

The words Jack heard could've been his imagination. Fortunately he knew better. "So am I."

All through the night Jack kept visiting the bedroom regularly although Ianto was never asleep. They didn't speak much but the silence didn't matter. Because they seemed to be close to reaching something far deeper.

Come morning, Ianto defied his injuries and Jack's protest and made them both a cup of coffee, as well as a light, meat free breakfast. Jack smiled as the taste swirled on his tongue. He hadn't realized how hungry he'd been. "Stuff of legends", he announced. They looked at each properly and saw. Like it'd been the first time.

Ianto didn't smile. But finally those eyes seemed alive, just a little bit. "Thank you, sir."

And for the first time since Lisa Jack felt hope that maybe, just maybe, Ianto could one day feel like a proper member of the team.

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><p>End of scene.<p>

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><p>AN: The desire to insert a scene like that to that episode's been sitting in my head since I first watched it! (chuckles) (Especially because something seemed to change between those two afterwards.) Poor Ianto! What a first mission…

Soooo… Any good, at all? PLEASE do leave a note to let me know! You can't even imagine how happy it'd make me.

NEXT ONE UP: There was a mention of rats in a certain episode that was left nagging me. Sooo, a deleted scene it is!  
>Thank you so much for reading! Who knows. Maybe I'll see you next time?<p>

Take care!


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